[mira_talk] Re: FW: 454 assembly
- From: Thomas Müller <thomas.mueller@xxxxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 22 Jul 2010 11:48:52 +0200
Sorry my bad!!!
I meant:
--job=denovo,genome,draft,454
cheers
Thomas
On Jul 22, 2010, at 11:36 AM, Shabhonam Caim (TGAC) wrote:
> Thanks thomas for your reply but still I am getting error:
> I have used the following command and provided the qual file as well :
>
> mira --project=test --job=denovo,genome,draft 454_SETTINGS
> -FN:fai=2.GAC.454Reads.fna -FN:fqui=2.GAC.454Reads.qual
>
> Minimum reads per group needed for tagging (mrpg) : [san] 2
> [454] 4
> Minimum neighbour quality needed for tagging (mnq) : [san] 20
> [454] 20
> Minimum Group Quality needed for RMB Tagging (mgqrt) : [san] 30
> [454] 25
> End-read Marking Exclusion Area in bases (emea) : [san] 25
> [454] 10
> Also mark gap bases (amgb) : [san] yes
> [454] no
> Also mark gap bases - even multicolumn (amgbemc) : [san] yes
> [454] yes
> Also mark gap bases - need both strands (amgbnbs): [san] yes
> [454] yes
> Force non-IUPAC consensus per sequencing type (fnicpst) : [san] no
> [454] no
> Merge short reads (msr) : [san] no
> [454] no
> Gap override ratio (gor) : [san] 66
> [454] 66
>
> Edit options (-ED):
> Automatic contig editing (ace) : [san] no
> [454] yes
> Sanger only:
> Strict editing mode (sem) : no
> Confirmation threshold in percent (ct) : 50
>
> Directories (-DI):
> When loading EXP files :
> When loading SCF files :
> Top directory for writing files : test_assembly
> For writing result files : test_assembly/test_d_results
> For writing result info files : test_assembly/test_d_info
> For writing log files : test_assembly/test_d_log
> For writing checkpoint files : test_assembly/test_d_chkpt
>
> File names (-FN):
> When loading sequences from FASTA : [san]
> test_in.sanger.fasta
> [454]
> 2.GAC.454Reads.fna
> When loading qualities from FASTA quality : [san]
> test_in.sanger.fasta.qual
> [454]
> 2.GAC.454Reads.qual
> When loading sequences from FASTQ : [san]
> test_in.sanger.fastq
> [454]
> test_in.454.fastq
> When loading project from CAF : test_in.sanger.caf
> When loading project from MAF (disabled) : test_in.sanger.maf
> When loading EXP fofn : test_in.fofn
> When loading project from PHD : test_in.phd.1
> When loading strain data : test_straindata_in.txt
> When loading XML trace info files : [san]
> test_traceinfo_in.sanger.xml
> [454]
> test_traceinfo_in.454.xml
> When loading SSAHA vector screen results :
> test_ssaha2vectorscreen_in.txt
>
> When loading backbone from MAF : test_backbone_in.maf
> When loading backbone from CAF : test_backbone_in.caf
> When loading backbone from GenBank : test_backbone_in.gbf
> When loading backbone from FASTA : test_backbone_in.fasta
>
>
> Output files (-OUTPUT/-OUT):
> Save simple singlets in project (sssip) : [san] no
> [454] no
> Save tagged singlets in project (stsip) : [san] yes
> [454] yes
>
> Remove rollover logs (rrol) : yes
> Remove log directory (rld) : no
>
> Result files:
> Saved as CAF (orc) : yes
> Saved as FASTA (orf) : yes
> Saved as GAP4 (directed assembly) (org) : no
> Saved as phrap ACE (ora) : yes
> Saved as HTML (orh) : no
> Saved as Transposed Contig Summary (ors) : yes
> Saved as simple text format (ort) : no
> Saved as wiggle (orw) : yes
>
> Temporary result files:
> Saved as CAF (otc) : yes
> Saved as CAF (otm) : no
> Saved as FASTA (otf) : no
> Saved as GAP4 (directed assembly) (otg) : no
> Saved as phrap ACE (ota) : no
> Saved as HTML (oth) : no
> Saved as Transposed Contig Summary (ots) : no
> Saved as simple text format (ott) : no
>
> Extended temporary result files:
> Saved as CAF (oetc) : no
> Saved as FASTA (oetf) : no
> Saved as GAP4 (directed assembly) (oetg) : no
> Saved as phrap ACE (oeta) : no
> Saved as HTML (oeth) : no
> Save also singlets (oetas) : no
>
> Alignment output customisation:
> TEXT characters per line (tcpl) : 60
> HTML characters per line (hcpl) : 60
> TEXT end gap fill character (tegfc) :
> HTML end gap fill character (hegfc) :
>
> File / directory output names:
> CAF : test_out.caf
> MAF : test_out.maf
> FASTA : test_out.unpadded.fasta
> FASTA quality : test_out.unpadded.fasta.qual
> FASTA (padded) : test_out.padded.fasta
> FASTA qual.(pad): test_out.padded.fasta.qual
> GAP4 (directory): test_out.gap4da
> ACE : test_out.ace
> HTML : test_out.html
> Simple text : test_out.txt
> TCS overview : test_out.tcs
> Wiggle : test_out.wig
> ------------------------------------------------------------------------------
> Deleting old directory test_assembly ... done.
> Creating directory test_assembly ... done.
> Creating directory test_assembly/test_d_log ... done.
> Creating directory test_assembly/test_d_results ... done.
> Creating directory test_assembly/test_d_info ... done.
> Creating directory test_assembly/test_d_chkpt ... done.
> Localtime: Thu Jul 22 10:31:49 2010
>
>
>
> ========================== Memory self assessment
> ==============================
> Running in 64 bit mode.
>
> Dump from /proc/meminfo
> --------------------------------------------------------------------------------
> MemTotal: 8174224 kB
> MemFree: 94968 kB
> Buffers: 4644 kB
> Cached: 4976444 kB
> SwapCached: 287504 kB
> Active: 6618732 kB
> Inactive: 1307228 kB
> HighTotal: 0 kB
> HighFree: 0 kB
> LowTotal: 8174224 kB
> LowFree: 94968 kB
> SwapTotal: 2031608 kB
> SwapFree: 1476740 kB
> Dirty: 1984 kB
> Writeback: 0 kB
> AnonPages: 2936468 kB
> Mapped: 32408 kB
> Slab: 81840 kB
> PageTables: 37252 kB
> NFS_Unstable: 0 kB
> Bounce: 0 kB
> CommitLimit: 6118720 kB
> Committed_AS: 5290616 kB
> VmallocTotal: 34359738367 kB
> VmallocUsed: 263728 kB
> VmallocChunk: 34359474579 kB
> HugePages_Total: 0
> HugePages_Free: 0
> HugePages_Rsvd: 0
> Hugepagesize: 2048 kB
> --------------------------------------------------------------------------------
>
> Dump from /proc/self/status
> --------------------------------------------------------------------------------
> Name: mira
> State: R (running)
> SleepAVG: 0%
> Tgid: 6158
> Pid: 6158
> PPid: 17617
> TracerPid: 0
> Uid: 8395 8395 8395 8395
> Gid: 3658 3658 3658 3658
> FDSize: 256
> Groups: 3658
> VmPeak: 4972 kB
> VmSize: 4920 kB
> VmLck: 0 kB
> VmHWM: 1744 kB
> VmRSS: 1744 kB
> VmData: 464 kB
> VmStk: 84 kB
> VmExe: 4336 kB
> VmLib: 0 kB
> VmPTE: 28 kB
> StaBrk: 00a7e000 kB
> Brk: 017f0000 kB
> StaStk: 7fffc798fa70 kB
> Threads: 1
> SigQ: 0/71680
> SigPnd: 0000000000000000
> ShdPnd: 0000000000000000
> SigBlk: 0000000000000000
> SigIgn: 0000000000000000
> SigCgt: 0000000180000000
> CapInh: 0000000000000000
> CapPrm: 0000000000000000
> CapEff: 0000000000000000
> Cpus_allowed:
> 00000000,00000000,00000000,00000000,00000000,00000000,00000000,000000ff
> Mems_allowed: 00000000,00000001
> --------------------------------------------------------------------------------
>
> Information on current assembly object:
>
> AS_readpool: 0 reads.
> AS_contigs: 0 contigs.
> AS_bbcontigs: 0 contigs.
> Mem used for reads: 112 (112 B)
>
> Memory used in assembly structures:
> Eff. Size Free cap. LostByAlign
> AS_writtenskimhitsperid: 0 24 B 0 B 0 B
> AS_skim_edges: 0 24 B 0 B 0 B
> AS_adsfacts: 0 24 B 0 B 0 B
> AS_confirmed_edges: 0 24 B 0 B 0 B
> AS_permanent_overlap_bans: 0 24 B 0 B 0 B
> AS_readhitmiss: 0 24 B 0 B 0 B
> AS_readhmcovered: 0 24 B 0 B 0 B
> AS_count_rhm: 0 24 B 0 B 0 B
> AS_clipleft: 0 24 B 0 B 0 B
> AS_clipright: 0 24 B 0 B 0 B
> AS_used_ids: 0 24 B 0 B 0 B
> AS_multicopies: 0 24 B 0 B 0 B
> AS_hasmcoverlaps: 0 24 B 0 B 0 B
> AS_maxcoveragereached: 0 24 B 0 B 0 B
> AS_coverageperseqtype: 0 24 B 0 B 0 B
> AS_istroublemaker: 0 24 B 0 B 0 B
> AS_isdebris: 0 24 B 0 B 0 B
> AS_needalloverlaps: 0 40 B 0 B 0 B
> AS_readsforrepeatresolve: 0 40 B 0 B 0 B
> AS_allrmbsok: 0 24 B 0 B 0 B
> AS_probablermbsnotok: 0 24 B 0 B 0 B
> AS_weakrmbsnotok: 0 24 B 0 B 0 B
> AS_readmaytakeskim: 0 40 B 0 B 0 B
> AS_skimstaken: 0 40 B 0 B 0 B
> AS_numskimoverlaps: 0 24 B 0 B 0 B
> AS_numleftextendskims: 0 24 B 0 B 0 B
> AS_rightextendskims: 0 24 B 0 B 0 B
> AS_skimleftextendratio: 0 24 B 0 B 0 B
> AS_skimrightextendratio: 0 24 B 0 B 0 B
> AS_usedlogfiles: 1 48 B 0 B 0 B
> Total: 920 (920 B)
>
> ================================================================================
> Dynamic allocs: 0
> Align allocs: 0
>
> Fatal Error (may be due to problems of the input data):
> "You did not specify any input sequences to be loaded."
>
> ->Thrown: void Assembly::loadSequenceData_new()
>
> ->Caught: main
>
> Cheers
> Shab
>
>
> From: mira_talk-bounce@xxxxxxxxxxxxx [mailto:mira_talk-bounce@xxxxxxxxxxxxx]
> On Behalf Of Thomas Müller
> Sent: 22 July 2010 10:12
> To: mira_talk@xxxxxxxxxxxxx
> Subject: [mira_talk] Re: FW: 454 assembly
>
> try:
> mira --project=test --job=denovo,genome,draft,est 454_SETTINGS
> -FN:fai=2.GAC.454Reads.fna
>
> But you should really also add the .qual file with FN:fqui=2.GAC.454Reads.qual
>
> cheers
> Thomas
>
> On Jul 22, 2010, at 10:53 AM, Shabhonam Caim (TGAC) wrote:
>
>
>
> Hello Mira Users
>
> I am trying to assemble the 454 reads using Mira by using following command:
> mira-3.0.0 mira --project=test --job=denovo,genome,draft,2.GAC.454Reads.fna
>
> and I am getting the following error:
>
> This is MIRA V3.0.0 (production version).
>
> Please cite: Chevreux, B., Wetter, T. and Suhai, S. (1999), Genome Sequence
> Assembly Using Trace Signals and Additional Sequence Information.
> Computer Science and Biology: Proceedings of the German Conference on
> Bioinformatics (GCB) 99, pp. 45-56.
>
> Mail general questions to the MIRA talk mailing list:
> mira_talk@xxxxxxxxxxxxx
>
> To (un-)subsubcribe the MIRA mailing lists, see:
> http://www.chevreux.org/mira_mailinglists.html
>
> To report bugs or ask for features, please use the new ticketing system at:
> http://sourceforge.net/apps/trac/mira-assembler/
> This ensures that requests don't get lost.
>
>
> Compiled by: bach
> Sun Jan 31 20:23:36 CET 2010
> On: Linux arcadia64 2.6.27-11-generic #1 SMP Wed Apr 1 20:53:41 UTC 2009
> x86_64 GNU/Linux
> Compiled in boundtracking mode.
> Compiled in bugtracking mode.
> Compilation settings (sorry, for debug):
> Size of size_t : 8
> Size of uint32 : 4
> Size of uint32_t: 4
> Size of uint64 : 8
> Size of uint64_t: 8
> Current system: Linux n57140 2.6.18-92.el5 #1 SMP Tue Apr 29 13:16:15 EDT
> 2008 x86_64 x86_64 x86_64 GNU/Linux
>
>
>
> Parsing parameters: --project=454asembly --job=denovo, genome, draft
> pk.454.fasta
>
> Seen no assembly quality in job definition, assuming 'normal'.
> Seen no assembly type in job definition, assuming 'genome'.
>
> ,..
>
> ========================= Parameter parsing error(s)
> ==========================
>
> * Parameter section: '(none)'
> * unrecognised string or unexpected character: genome
>
> * Parameter section: '(none)'
> * unrecognised string or unexpected character: draft
>
> * Parameter section: '(none)'
> * unrecognised string or unexpected character: pk
>
> * Parameter section: '(none)'
> * unrecognised string or unexpected character: 454
>
> * Parameter section: '(none)'
> * unrecognised string or unexpected character: fasta
>
> ===============================================================================
>
> Fatal Error (may be due to problems of the input data):
> "Error while parsing parameters, sorry."
>
> ->Thrown: void MIRAParameters::parse(istream & is, vector<MIRAParameters> &
> Pv, MIRAParameters * singlemp)
>
> ->Caught: main
>
> Or can I please get the commands to run the 454 assembly (basic denovo
> assembly with default parameters)
>
> cheers
>
> Shab
>
>
> --
> Crop Plant Biodiversity and Breeding Informatics Group (350b)
> Institute of Plant Breeding, Seed Science and Population Genetics
> University of Hohenheim
> Fruwirthstrasse 21
> D-70599 Stuttgart
> Phone: +49-711-459 24293
>
--
Crop Plant Biodiversity and Breeding Informatics Group (350b)
Institute of Plant Breeding, Seed Science and Population Genetics
University of Hohenheim
Fruwirthstrasse 21
D-70599 Stuttgart
Phone: +49-711-459 24293
Other related posts:
